Caulobacter crescentus is a non-pathogenic, gram-negative bacterium that serves as a powerful model system for understanding the cell cycle and asymmetric cell division. We have developed a set of systematic genetic and biochemical tools to map two-component signal transduction pathways in Caulobacter. Two-component signal transduction, comprised of histidine kinases and response regulators, allows bacteria to sense and respond to their environment. Using a systems-level approach, we have rapidly identified pathways which control growth, morphogenesis, and cell cycle progression. Our methods are generally applicable to all bacteria which use this mode of signal transduction. In addition, we have uncovered fundamental principles of two-component signal transduction which explain how pathways remain insulated in vivo. Caulobacter, a member of the a-proteobacteria, is closely related to Zymomonas mobilis. How the knowledge gained in Caulobacter, and the tools we have developed, can be applied to bacteria important for lignocellulose biodegradation and ethanol production will be discussed.